mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| MC | CP000731 | 1 | Δ27,041 bp | 100% | repA–USA300HOU_pUSA300HOUMR0033 | 26 genes repA, USA300HOU_pUSA300HOUMR0003, USA300HOU_pUSA300HOUMR0004, USA300HOU_pUSA300HOUMR0005, USA300HOU_pUSA300HOUMR0006, cadR, cadX, USA300HOU_pUSA300HOUMR0010, blaZ, blaR, blaI, USA300HOU_pUSA300HOUMR0014, USA300HOU_pUSA300HOUMR0015, USA300HOU_pUSA300HOUMR0016, USA300HOU_pUSA300HOUMR0018, USA300HOU_pUSA300HOUMR0019, USA300HOU_pUSA300HOUMR0021, USA300HOU_pUSA300HOUMR0023, USA300HOU_pUSA300HOUMR0024, USA300HOU_pUSA300HOUMR0027, USA300HOU_pUSA300HOUMR0028, USA300HOU_pUSA300HOUMR0029, USA300HOU_pUSA300HOUMR0030, USA300HOU_pUSA300HOUMR0031, USA300HOU_pUSA300HOUMR0032, USA300HOU_pUSA300HOUMR0033 |
|
| RA | USA300TCH1516_ALE | 5,952 | C→T | 9.2% | R298C (CGT→TGT) | gyrB → | DNA gyrase subunit B |
| RA | USA300TCH1516_ALE | 19,009 | C→T | 100% | S222F (TCC→TTC) | gdpP → | Cyclic‑di‑AMP phosphodiesterase GdpP |
| RA | USA300TCH1516_ALE | 39,653 | C→A | 100% | S494I (AGT→ATT) | pbp ← | Beta‑lactam‑inducible penicillin‑binding protein |
| RA | USA300TCH1516_ALE | 41,171 | T→C | 6.5% | intergenic (‑38/‑62) | pbp ← / → mecR1 | Beta‑lactam‑inducible penicillin‑binding protein/Methicillin resistance mecR1 protein |
| RA | USA300TCH1516_ALE | 51,740 | C→A | 8.6% | Q134K (CAA→AAA) | USA300HOU_RS00215 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 110,651 | C→T | 6.3% | D170D (GAC→GAT) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 110,660 | T→A | 13.1% | I173I (ATT→ATA) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 110,904 | G→T | 44.5% | D255Y (GAT→TAT) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,329 | T→A | 8.3% | N133K (AAT→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 37.9% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 36.4% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,560 | T→C | 15.7% | R210R (CGT→CGC) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,572 | C→T | 6.3% | D214D (GAC→GAT) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 119,853 | C→A | 51.8% | G254W (GGG→TGG) | USA300HOU_RS00550 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 253,983 | A→G | 6.7% | intergenic (+196/+166) | asbF → / ← USA300HOU_RS01125 | 3‑dehydroshikimate dehydratase/hypothetical protein |
| RA | USA300TCH1516_ALE | 253,984 | G→T | 7.1% | intergenic (+197/+165) | asbF → / ← USA300HOU_RS01125 | 3‑dehydroshikimate dehydratase/hypothetical protein |
| RA | USA300TCH1516_ALE | 328,487 | C→A | 11.3% | I210I (ATC→ATA) | USA300HOU_RS01470 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 478,502 | C→A | 100% | D342E (GAC→GAA) | nuoL → | NADH‑quinone oxidoreductase subunit L |
| RA | USA300TCH1516_ALE | 492,848 | A→T | 5.4% | F62Y (TTC→TAC) | USA300HOU_RS02345 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 503,565 | G→A | 7.5% | noncoding (20/93 nt) | USA300TCH1516_00452 → | tRNA‑Ser |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 48.5% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 584,121 | G→T | 100% | intergenic (+205/‑67) | rplA → / → rplJ | 50S ribosomal protein L1/50S ribosomal protein L10 |
| RA | USA300TCH1516_ALE | 589,532 | G→T | 7.9% | D1146Y (GAT→TAT) ‡ | rpoB → | DNA‑directed RNA polymerase subunit beta |
| RA | USA300TCH1516_ALE | 589,533 | A→T | 8.1% | D1146V (GAT→GTT) ‡ | rpoB → | DNA‑directed RNA polymerase subunit beta |
| RA | USA300TCH1516_ALE | 602,466 | G→T | 15.8% | intergenic (+56/‑104) | hchA → / → araB | Molecular chaperone Hsp31 and glyoxalase 3/Ribulokinase |
| RA | USA300TCH1516_ALE | 618,588 | G→A | 9.5% | S1230S (TCG→TCA) | sdrD → | Serine‑aspartate repeat‑containing protein D |
| RA | USA300TCH1516_ALE | 618,759 | T→C | 6.8% | D1287D (GAT→GAC) | sdrD → | Serine‑aspartate repeat‑containing protein D |
| RA | USA300TCH1516_ALE | 622,464 | G→A | 11.2% | S1009S (TCG→TCA) | sdrE → | Serine‑aspartate repeat‑containing protein E |
| RA | USA300TCH1516_ALE | 622,479 | T→C | 6.5% | D1014D (GAT→GAC) | sdrE → | Serine‑aspartate repeat‑containing protein E |
| RA | USA300TCH1516_ALE | 622,521 | T→C | 6.2% | D1028D (GAT→GAC) | sdrE → | Serine‑aspartate repeat‑containing protein E |
| RA | USA300TCH1516_ALE | 622,536 | G→A | 7.8% | S1033S (TCG→TCA) | sdrE → | Serine‑aspartate repeat‑containing protein E |
| RA | USA300TCH1516_ALE | 691,587 | G→T | 7.3% | Q79K (CAA→AAA) | USA300HOU_RS03335 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 707,909 | A→T | 100% | M1M (TTG→ATG) † | znuC_1 ← | High‑affinity zinc uptake system ATP‑binding protein ZnuC |
| RA | USA300TCH1516_ALE | 849,656 | G→A | 56.7% | G261D (GGT→GAT) | USA300HOU_RS04145 → | Nucleotide‑binding protein |
| RA | USA300TCH1516_ALE | 937,158 | T→A | 5.6% | intergenic (+65/‑66) | USA300HOU_RS04665 → / → pepA_1 | NADH dehydrogenase‑like protein/Cytosol aminopeptidase |
| RA | USA300TCH1516_ALE | 973,213 | C→A | 100% | E175* (GAG→TAG) | yitU_1 ← | 5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase YitU |
| RA | USA300TCH1516_ALE | 1,002,200 | T→G | 100% | M173R (ATG→AGG) | mecA → | Adapter protein MecA 1 |
| RA | USA300TCH1516_ALE | 1,055,126 | T→G | 5.2% | T352T (ACA→ACC) | patA_2 ← | Putative N‑acetyl‑LL‑diaminopimelate aminotransferase |
| RA | USA300TCH1516_ALE | 1,105,994 | T→C | 100% | T12T (ACT→ACC) | pdhD → | Dihydrolipoyl dehydrogenase |
| RA | USA300TCH1516_ALE | 1,196,508 | C→A | 100% | S338Y (TCT→TAT) | ftsZ → | Cell division protein FtsZ |
| RA | USA300TCH1516_ALE | 1,231,411 | A→G | 100% | D19G (GAT→GGT) | stp → | Serine/threonine phosphatase stp |
| RA | USA300TCH1516_ALE | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD_4 ← | Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,425,560 | G→T | 8.5% | P237H (CCT→CAT) | pstS ← | Phosphate‑binding protein PstS |
| RA | USA300TCH1516_ALE | 1,472,936 | A→T | 6.6% | A9696A (GCT→GCA) | ebh_1 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 1,513,930 | A→T | 100% | L413F (TTA→TTT) | USA300HOU_RS07375 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,539,250 | C→G | 100% | intergenic (‑349/+37) | aroC ← / ← USA300HOU_RS07505 | Chorismate synthase/hypothetical protein |
| RA | USA300TCH1516_ALE | 1,643,049 | G→A | 23.5% | A341V (GCT→GTT) | cfiB_2 ← | 2‑oxoglutarate carboxylase small subunit |
| RA | USA300TCH1516_ALE | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | ypdF ← | Aminopeptidase YpdF |
| RA | USA300TCH1516_ALE | 1,744,473 | C→T | 100% | A67T (GCT→ACT) | apt ← | Adenine phosphoribosyltransferase |
| JC | USA300TCH1516_ALE | 1,747,374 | Δ3 bp | 52.7% | coding (2073‑2075/2280 nt) | USA300HOU_RS08710 ← | Heme uptake protein MmpL11 |
| RA | USA300TCH1516_ALE | 1,857,867 | C→T | 12.2% | L169L (TTG→TTA) | USA300HOU_RS09235 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,909,214 | C→A | 47.4% | Y7* (TAC→TAA) | USA300HOU_RS09460 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,945,299 | G→T | 6.1% | intergenic (‑880/‑84) | splA ← / → USA300HOU_RS09665 | Serine protease SplA/hypothetical protein |
| RA | USA300TCH1516_ALE | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
| RA | USA300TCH1516_ALE | 2,027,805 | C→A | 100% | V48F (GTT→TTT) | vraS ← | Sensor protein VraS |
| RA | USA300TCH1516_ALE | 2,172,075 | G→C | 5.1% | E42Q (GAA→CAA) | leuB → | 3‑isopropylmalate dehydrogenase |
| RA | USA300TCH1516_ALE | 2,172,078 | T→A | 5.3% | F43I (TTT→ATT) | leuB → | 3‑isopropylmalate dehydrogenase |
| RA | USA300TCH1516_ALE | 2,172,081 | G→C | 5.4% | G44R (GGT→CGT) | leuB → | 3‑isopropylmalate dehydrogenase |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | 100% | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,291,888 | G→A | 5.6% | K813K (AAG→AAA) | USA300HOU_RS11675 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,337,959 | C→T | 100% | intergenic (‑125/‑283) | adhR ← / → USA300HOU_RS11940 | HTH‑type transcriptional regulator AdhR/Hyaluronate lyase |
| RA | USA300TCH1516_ALE | 2,342,818 | T→A | 5.1% | intergenic (‑213/‑81) | USA300HOU_RS11950 ← / → USA300HOU_RS11955 | putative hydrolase/65 kDa membrane protein |
| RA | USA300TCH1516_ALE | 2,343,438 | C→T | 100% | intergenic (+114/+250) | USA300HOU_RS11955 → / ← aldC_1 | 65 kDa membrane protein/Alpha‑acetolactate decarboxylase |
| RA | USA300TCH1516_ALE | 2,361,590 | C→T | 50.0% | R239H (CGT→CAT) | secY ← | Protein translocase subunit SecY |
| RA | USA300TCH1516_ALE | 2,451,405 | G→T | 8.5% | Q5K (CAA→AAA) | hutU ← | Urocanate hydratase |
| RA | USA300TCH1516_ALE | 2,455,692 | Δ1 bp | 100% | coding (1210/1260 nt) | lyrA → | Lysostaphin resistance protein A |
| RA | USA300TCH1516_ALE | 2,455,698 | 2 bp→AT | 100% | coding (1216‑1217/1260 nt) | lyrA → | Lysostaphin resistance protein A |
| RA | USA300TCH1516_ALE | 2,504,989 | T→C | 7.2% | intergenic (+293/+111) | USA300HOU_RS12890 → / ← gltT | hypothetical protein/Proton/sodium‑glutamate symport protein |
| RA | USA300TCH1516_ALE | 2,519,951 | T→G | 5.5% | P227P (CCA→CCC) | narG ← | Respiratory nitrate reductase 1 alpha chain |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,626,838 | A→T | 9.7% | D75E (GAT→GAA) | sarT ← | HTH‑type transcriptional regulator SarT |
| RA | USA300TCH1516_ALE | 2,774,981 | A→G | 6.7% | D735D (GAT→GAC) | clfB ← | Clumping factor B |
| RA | USA300TCH1516_ALE | 2,775,029 | G→A | 5.1% | D719D (GAC→GAT) | clfB ← | Clumping factor B |
| RA | USA300TCH1516_ALE | 2,775,041 | A→G | 6.3% | D715D (GAT→GAC) | clfB ← | Clumping factor B |
| RA | USA300TCH1516_ALE | 2,775,053 | A→G | 7.0% | D711D (GAT→GAC) | clfB ← | Clumping factor B |
| RA | USA300TCH1516_ALE | 2,854,538 | T→A | 5.8% | intergenic (+236/+177) | yflS → / ← USA300HOU_RS14625 | Putative malate transporter YflS/hypothetical protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 34173 = | 131 (0.940) | 12 (0.090) | 12/246 | NT | 8.0% | coding (462/480 nt) | rlmH | Ribosomal RNA large subunit methyltransferase H |
| ? | USA300TCH1516_ALE | = 57858 | 151 (1.130) | intergenic (+304/+613) | USA300HOU_RS00240/USA300TCH1516_00049 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 512620 = | 185 (1.320) | 110 (1.140) +40 bp |
72/178 | NT | 46.4% | intergenic (+688/‑6075) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| ? | USA300TCH1516_ALE | 1998278 = | NA (NA) | intergenic (‑6/+3329) | USA300TCH1516_01882/USA300TCH1516_01883 | tRNA‑Val/tRNA‑Ala | |||||
| * | ? | USA300TCH1516_ALE | 528464 = | 96 (0.690) | 7 (0.060) | 5/230 | NT | 7.3% | intergenic (+5/‑162) | dtd3/rnmV_1 | D‑aminoacyl‑tRNA deacylase/Ribonuclease M5 |
| ? | USA300TCH1516_ALE | 528541 = | 92 (0.740) | intergenic (+82/‑85) | dtd3/rnmV_1 | D‑aminoacyl‑tRNA deacylase/Ribonuclease M5 | |||||
| * | ? | USA300TCH1516_ALE | = 528477 | 99 (0.710) | 5 (0.040) | 5/230 | NT | 5.3% | intergenic (+18/‑149) | dtd3/rnmV_1 | D‑aminoacyl‑tRNA deacylase/Ribonuclease M5 |
| ? | USA300TCH1516_ALE | = 528526 | 92 (0.740) | intergenic (+67/‑100) | dtd3/rnmV_1 | D‑aminoacyl‑tRNA deacylase/Ribonuclease M5 | |||||
| * | ? | USA300TCH1516_ALE | 854380 = | 116 (0.830) | 7 (0.050) | 6/246 | NT | 6.0% | intergenic (‑275/‑460) | USA300HOU_RS04170/zipA_1 | Epimerase family protein/Cell division protein ZipA |
| ? | USA300TCH1516_ALE | 854405 = | 110 (0.830) | intergenic (‑300/‑435) | USA300HOU_RS04170/zipA_1 | Epimerase family protein/Cell division protein ZipA | |||||
| * | ? | USA300TCH1516_ALE | = 1443583 | 98 (0.700) | 5 (0.040) | 3/248 | NT | 6.6% | intergenic (‑156/+197) | USA300TCH1516_01342/brnQ_3 | hypothetical protein/Branched‑chain amino acid transport system 2 carrier protein |
| ? | USA300TCH1516_ALE | 2317554 = | 48 (0.360) | intergenic (+207/‑249) | iucC_3/USA300TCH1516_02193 | Aerobactin synthase/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 1929987 = | 132 (0.940) | 7 (0.060) | 7/232 | NT | 5.8% | intergenic (‑323/+547) | USA300TCH1516_01793/USA300HOU_RS09600 | hypothetical protein/hypothetical protein |
| ? | USA300TCH1516_ALE | 1930020 = | 107 (0.850) | intergenic (‑356/+514) | USA300TCH1516_01793/USA300HOU_RS09600 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 2181210 = | 121 (0.870) | 7 (0.050) | 6/240 | NT | 5.9% | intergenic (+4972/+323) | ilvA/USA300TCH1516_02069 | L‑threonine dehydratase biosynthetic IlvA/tRNA‑Gly |
| ? | USA300TCH1516_ALE | 2297542 = | NA (NA) | intergenic (‑4794/+639) | USA300TCH1516_02176/salA | tRNA‑Asn/Iron‑sulfur cluster carrier protein | |||||
| * | ? | USA300TCH1516_ALE | 2388283 = | 160 (1.140) | 7 (0.060) | 7/224 | NT | 5.1% | intergenic (+18/+84) | ribZ_1/sarV | Riboflavin transporter RibZ/HTH‑type transcriptional regulator SarV |
| ? | USA300TCH1516_ALE | 2388362 = | 121 (1.000) | intergenic (+97/+5) | ribZ_1/sarV | Riboflavin transporter RibZ/HTH‑type transcriptional regulator SarV | |||||
| * | ? | USA300TCH1516_ALE | 2679162 = | 153 (1.090) | 8 (0.060) | 6/246 | NT | 5.2% | intergenic (+34/‑355) | USA300HOU_RS13790/ssaA2_4 | hypothetical protein/Staphylococcal secretory antigen ssaA2 |
| ? | USA300TCH1516_ALE | 2679186 = | 147 (1.100) | intergenic (+58/‑331) | USA300HOU_RS13790/ssaA2_4 | hypothetical protein/Staphylococcal secretory antigen ssaA2 | |||||
| * | ? | USA300TCH1516_ALE | 2693368 = | 120 (0.860) | 7 (0.060) | 6/234 | NT | 6.5% | intergenic (+39/+317) | mtrR/rocA | HTH‑type transcriptional regulator MtrR/1‑pyrroline‑5‑carboxylate dehydrogenase |
| ? | USA300TCH1516_ALE | 2693417 = | 93 (0.730) | intergenic (+88/+268) | mtrR/rocA | HTH‑type transcriptional regulator MtrR/1‑pyrroline‑5‑carboxylate dehydrogenase | |||||